RNAUP

NAME

RNAup −
manual page for RNAup 2.4.0

SYNOPSIS

RNAup
[OPTIONS]...

DESCRIPTION

RNAup 2.4.0

Calculate the
thermodynamics of RNA−RNA interactions

RNAup
calculates the thermodynamics of RNA−RNA interactions,
by decomposing the binding into two stages. (1) First the
probability that a potential binding sites remains unpaired
(equivalent to the free energy needed to open the site) is
computed. (2) Then this accessibility is combined with the
interaction energy to obtain the total binding energy. All
calculations are done by computing partition functions over
all possible conformations.

RNAup provides
two different modes: By default RNAup computes
accessibilities, in terms of the free energies needed to
open a region (default length 4). It prints the region of
highest accessibility and its opening energy to stdout,
opening energies for all other regions are written to a
file.

In interaction
mode the interaction between two RNAs is calculated. It is
invoked if the input consists of two sequences concatenated
with an "&", or if the options -X[pf] or -b
are given. Unless the -b option is specified RNAup assumes
that the longer RNA is a structured target sequence while
the shorter one is an unstructured small RNA.
Additionally, for every position along the target sequence
we write the best free energy of binding for an interaction
that includes this position to the the output file. Output
to stdout consists of the location and free energy, dG, for
the optimal region of interaction. The binding energy dG is
also split into its components the interaction energy dGint
and the opening energy dGu_l (and possibly dGu_s for the
shorter sequence).
In addition we print the optimal interaction structure as
computed by RNAduplex for this region. Note that it can
happen that the RNAduplex computed optimal interaction does
not coincide with the optimal RNAup region. If the two
predictions don’t match the structure string is
replaced by a run of "." and a message is written
to stderr.

Each sequence
should be in 5’ to 3’ direction. If the sequence
is preceded by a line of the form

> name

the output file
"name_ux_up.out" is produced, where the
"x" in "ux" is the value set by the -u
option. Otherwise the file name defaults to RNA_ux_up.out.
The output is concatenated if a file with the same name
exists.

RNA sequences
are read from stdin as strings of characters. White space
and newline within a sequence cause an error! Newline is
used to separate sequences. The program will continue to
read new sequences until a line consisting of the single
character @ or an end of file condition is encountered.
−h, −−help

Print help and exit

−−detailed−help

Print help, including all
details and hidden options, and exit

−−full−help

Print help, including hidden
options, and exit

−V,
−−version

Print version and exit

General
Options:

Below are command line options
which alter the general behavior of this program

−C,
−−constraint

Calculate structures subject to
constraints. (default=off)

The program
reads first the sequence(s), then a string containing
constraints on the structure encoded with the symbols:

. (no
constraint for this base)

x (the base is
unpaired) < (base i is paired with a base j>i) (solely
used for calculation of

unpaired
regions)

> (base
i is paired with a base j<i) (solely used for calculation
of

unpaired
regions)

( ) (base i
pairs base j) | (the corresponding base has to be paired
intermolecularily (works only in

interaction
mode)

−o,
−−no_output_file

Do not produce an output
file

(default=off)

−−no_header

Do not produce a header with
the command line parameters used in the outputfile

(default=off)

−−noconv

Do not automatically substitude
nucleotide "T" with "U"

(default=off)

Calculations
of opening energies:
−u, −−ulength=length

specifies the length of the
unstructured region in the output.

(default=‘4’)

The probability
of being unpaired is plotted on the right border of the
unpaired region. You can specify up to 20 different length
values: use "−" to specify a range of
continuous values (e.g. −u 4−8) or
specify a list of comma separated values (e.g.
−u 4,8,15).

−c,
−−contributions=SHIME

Specify the contributions
listed in the output (default=‘S’)

By default only
the full probability of being unpaired is plotted. The
−c option allows one to get the different
contributions (c) to the probability of being unpaired: The
full probability of being unpaired ("S" is the sum
of the probability of being unpaired in the exterior loop
("E"), within a hairpin loop ("H"),
within an interior loop ("I") and within a
multiloop ("M"). Any combination of these letters
may be given.

Calculations
of RNA-RNA interactions:
−w, −−window=INT

Determine the maximal length of
the region of interaction

(default=‘25’)

−b,
−−include_both

Include the probability of
unpaired regions in both (b) RNAs. By default only the
probability of being unpaired in the longer RNA (target) is
used.

(default=off)

−5,
−−extend5=INT

Extend the region of
interaction in the target to some residues on the 5’
side

The underlying
assumption is that it is favorable for an interaction if not
only the direct region of contact is unpaired but also a few
residues 5’

−3,
−−extend3=INT

Extend the region of
interaction in the target to some residues on the 3’
side

The underlying
assumption is that it is favorable for an interaction if not
only the direct region of contact is unpaired but also a few
residues 3’

−−interaction_pairwise

Activate pairwise interaction
mode (default=off)

The first
sequence interacts with the 2nd, the third with the 4th etc.
If activated, two interacting sequences may be given in a
single line separated by "&" or each sequence
may be given on an extra line.

−−interaction_first

Activate interaction mode using
first sequence only

(default=off)

The interaction
of each sequence with the first one is calculated (e.g.
interaction of one mRNA with many small RNAs). Each sequence
has to be given on an extra line

Model
Details:
−S, −−pfScale=DOUBLE

In the calculation of the pf
use scale*mfe as an estimate for the ensemble free energy
(used to avoid overflows). The default is 1.07, useful
values are 1.0 to 1.2. Occasionally needed for long
sequences. You can also recompile the program to use double
precision (see the README file).

−T,
−−temp=DOUBLE

Rescale energy parameters to a
temperature of temp C. Default is 37C.

−4,
−−noTetra

Do not include special
tabulated stabilizing energies for tri−, tetra−
and hexaloop hairpins. Mostly for testing.

(default=off)

−d,
−−dangles=INT

How to treat "dangling
end" energies for bases adjacent to helices in free
ends and multi−loops

(default=‘2’)

With
−d2 dangling energies will be added for the
bases adjacent to a helix on both sides in any case.

For partition
function folding this only disallows pairs that can only
occur isolated. Other pairs may still occasionally occur as
helices of length 1.

−−noGU

Do not allow GU pairs

(default=off)

−−noClosingGU

Do not allow GU pairs at the
end of helices

(default=off)

−P,
−−paramFile=paramfile

Read energy parameters from
paramfile, instead of using the default parameter set.

A sample
parameter file should accompany your distribution. See the
RNAlib documentation for details on the file format.

−−nsp=STRING

Allow other pairs in addition
to the usual AU,GC,and GU pairs.

Its argument is
a comma separated list of additionally allowed pairs. If the
first character is a "−" then AB will imply
that AB and BA are allowed pairs. e.g. RNAfold −nsp
−GA will allow GA and AG pairs. Nonstandard pairs
are given 0 stacking energy.

−e,
−−energyModel=INT

Rarely used option to fold
sequences from the artificial ABCD... alphabet, where A
pairs B, C−D etc. Use the energy parameters for GC
(−e 1) or AU (−e 2) pairs.

EXAMPLES

Output to
stdout:

In Interaction
mode RNAup prints the most favorable interaction energy
between the two sequences to stdout. The most favorable
interaction energy (dG) depends on the position in the
longer sequence (region [i,j]) and the position in the
shorter sequence (region[k,l]): dG[i,j;k,l]. dG[i,j;k,l] is
the largest contribution to dG[i,j] = sum_kl dG[i,j;k,l]
which is given in the output file: therefore dG[i,j;k,l]
<= dG[i,j].

Output to file
contains a header including date, the command line of the
call to RNAup, length and names of the input sequence(s)
followed by the sequence(s). The first sequence is the
target sequence. Printing of the header can be turned off
using the -nh option.

The line
directly after the header gives the column names for the
output:

position dGu_l for -u 3 dGu_l for -u 4 dG
# pos u3S u3H u4S u4H dG

where all
information refers to the target sequence. The dGu_l column
contains information about the -u value (u=3 or u=4) and the
contribution to the free energy to open all structures
"S" or only hairpin loops "H", see
option -c. NA means that no results is possible (e.g. column
u3S row 2: no region of length 3 ending at position 2
exists).